From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Fri Sep 27 2013 - 13:30:35 CDT
I have little experience with nanoparticles, but it seems that there also
exists a GolP version that is compatible with the CHARMM force field:
L. B. Wright et al., J. Chem. Theory Comput. 2013, 9, 1616–1630
http://pubs.acs.org/doi/pdf/10.1021/ct301018m
On 09/27/2013 04:10 AM, Luca Bellucci wrote:
> Hi Eddie,
> you can find a version of GolP here:
>
> http://web.fisica.unimo.it/prosurf/download/download.php
>
> It is worth noting that GOLP describe the interaction betwenn biomolecules
> (OPLS) and gold SURFACE and NOT Naoparticles. It is defined with the same
> potential-energy functions of the OPLS FF, therefore it is compatible with
> bio-oriented MD codes and it includes a polarization effect due to
> image charges induced by the adsorbed charge.
>
> CHARMM formatof GOLP for NAMD is not present for the download,
> however, I can send topology, parameters and tutorial privately.
>
> Luca
>
>> Thank you all so much for your help!!! I really appreciate the references,
>> suggestions, clarifications and offers. It sounds like GoIP will do what
>> I'd like to try and I think that will let me create and model the system I
>> have in mind. Please let me know how I can obtain GoIP.
>> Thanks again for all your help!
>> Eddie
>>
>> On Thu, Sep 26, 2013 at 4:07 AM, lcbllcc_at_gmail.com <lcbllcc_at_gmail.com>wrote:
>>> Hi all,
>>>
>>> if you are interested, we have GolP ( Gold parameter + OPLS/AA
>>> parmetrized by Corni and Iori) in CHARMM format, which can be used with
>>> NAMD.
>>> Golp FF: is an atomistic FF to model Gold Surface and protein
>>> (OPLS/AA) ; image effect ("metal polarization") is also included.
>>>
>>> Best,
>>>
>>> Luca
>>>
>>>> Hi Eddie,
>>>>
>>>> You might want to look at these two approaches to model gold, both of
>>>> which are classical and should work with NAMD. In the first approach
>>>> (see papers by Ana Vila Verde and Janna Maranas,
>>>> http://pubs.acs.org/doi/abs/10.1021/bm9002464 and
>>>> http://dx.doi.org/10.1021/la104814z) the gold model is a simple LJ
>>>> potential; this approach, while simplistic, works well if you are
>>>> interested in a system with many charges (like, say,
>>>> water+ions+proteins adsorbing on gold) because the image charge
>>>> interactions largely cancel out. If you choose to go this way, I have
>>>> a script to produce a psf file for gold that would be a useful
>>>> starting point for you. The script is clunky, though, so you might be
>>>> better off using the topotools tool like Axel said...
>>>>
>>>> The second approach involves a classical representation of gold
>>>> polarizability (see papers by Stefano Corni and E. Iori,
>>>> http://onlinelibrary.wiley.com/doi/10.1002/jcc.21165/abstract and
>>>> http://pubs.acs.org/doi/abs/10.1021/la904765u). You can try emailing
>>>> the authors to see if they have any files/scripts to run simulations in
>>>> NAMD before you start reinventing wheels in this case. I met some of
>>>> the authors and they are very approachable.
>>>>
>>>> I hope this helps. Best,
>>>>
>>>> Ana
>>>>
>>>> On 9/25/13 7:37 PM, Axel Kohlmeyer wrote:
>>>>> On Wed, Sep 25, 2013 at 6:52 PM, Dr. Eddie <eackad_at_gmail.com> wrote:
>>>>>> I thought the protein would be the hard part...
>>>>>>
>>>>>> In the end I would like to look at effect the nanoparticles have on
>>>
>>> ordering
>>>
>>>>>> the system. Thus, to the best I can see right now, I would want the
>>>>>> course-grain model to include a local and global approximation to
>>>>>> the nanoparticle's electric field and surface polarizability due to
>>>>>> water
>>>
>>> and
>>>
>>>>>> the proteins. I only expect the gold nanoparticle to interact via
>>>
>>> high order
>>>
>>>>>> electric moments, that depend on its shape, with the proteins. Is
>>>
>>> that way
>>>
>>>>>> off the mark?
>>>>>
>>>>> i don't know. i am not an expert in that field. it looks to me like a
>>>>> multi-scale problem, where you need more than just one kind of
>>>>> calculation, but need to build a coarser scale model based on the
>>>>> previous level and - if available - validate it with suitable
>>>>> experimental data. you mention polarization, but i would expect that
>>>>> this would be mostly determined by the surrounding solvation shell
>>>>> and attached molecules, so there is a good chance that this could be
>>>>> very well approximated with a non-polarizable all-atom model. there
>>>>> is the group of gary grest at sandia that does pretty big
>>>>> simulations related to that. perhaps, there is something you can
>>>>> learn from their publications.
>>>>>
>>>>> not sure how you can coarse grain this efficiently. and specifically
>>>>> include electrostatics well enough. it is possible to fit a
>>>>> multi-pole expansion to a set of point charges.
>>>>>
>>>>> at the higher level, you probably need something that is purely shape
>>>>> based and has an efficient to compute solvent. martini style coarse
>>>>> graining may be not enough for a reasonably large system, but could
>>>>> be used at an intermediate step.
>>>>>
>>>>> at the high level, it looks like you want to use something that
>>>>> models particles purely based on shape, but with a choice of shape
>>>>> variation. that would require either an implicit solvent via
>>>>> brownian dynamics or you could look at stochastic rotation dynamics
>>>>> (SRD). the group of sharon glotzer does work on "shaped
>>>>> nanoparticles", so perhaps you can steal some good ideas from them.
>>>>>
>>>>> there are likely many more people working on aspects of these kind of
>>>>> systems. i doubt that you will get something useful by just setting
>>>>> up a system with "some model" and let it go. this rarely works. MD
>>>>> simulations almost always need "a plan(tm)".
>>>>>
>>>>> axel.
>>>>>
>>>>>> In the end I will be trying to replicate a colleagues experimental
>>>
>>> results
>>>
>>>>>> of order inducement as a function of gold nanopartcile concentration
>>>
>>> and
>>>
>>>>>> other measures.
>>>>>>
>>>>>> Thanks again!
>>>>>> Eddie
>>>>>>
>>>>>>
>>>>>> On Wed, Sep 25, 2013 at 11:34 AM, Axel Kohlmeyer
>>>>>> <akohlmey_at_gmail.com>
>>>
>>> wrote:
>>>>>>> On Wed, Sep 25, 2013 at 6:25 PM, Dr. Eddie <eackad_at_gmail.com> wrote:
>>>>>>>> Hi all,
>>>>>>>> I would like to use namd to perform a simulation with coarse-grain
>>>>>>>> proteins
>>>>>>>> around gold nanoparticles. I see vmd has a coarse grain model
>>>
>>> builder so
>>>
>>>>>>>> that leaves the gold nanopartciles. Are there any tools for
>>>>>>>> building these
>>>>>>>> nanoparticles and generating their psf using the charmm
>>>>>>>> forcefield?
>>>
>>> I
>>>
>>>>>>> do you have an idea how you want to model / coarse grain the gold
>>>>>>> atoms? and how the interaction between the proteins and the gold
>>>>>>> particle? just having a tool to build the coarse grain model for
>>>>>>> the proteins, is the least of your problems.
>>>>>>>
>>>>>>> building custom psf files from scripting can be done with the
>>>
>>> topotools
>>>
>>>>>>> plugin.
>>>>>>>
>>>>>>> axel.
>>>>>>>
>>>>>>>> thought I'd ask before reinventing the wheel so to speak.
>>>>>>>> Thanks!
>>>>>>>> Eddie
>>>>>>>
>>>>>>> --
>>>>>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>>>>>>> International Centre for Theoretical Physics, Trieste. Italy.
>>>>>>
>>>>>> --
>>>>>> Eddie
>
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